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- PDB-9wkr: structure of human propionyl-coenzyme A carboxylase in BC binding... -

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Basic information

Entry
Database: PDB / ID: 9wkr
Titlestructure of human propionyl-coenzyme A carboxylase in BC binding state
Components
  • Propionyl-CoA carboxylase alpha chain, mitochondrial
  • Propionyl-CoA carboxylase beta chain, mitochondrial
KeywordsCYTOSOLIC PROTEIN / PCC / Mitochondrial
Function / homology
Function and homology information


branched-chain amino acid metabolic process / succinyl-CoA biosynthetic process / Propionyl-CoA catabolism / short-chain fatty acid catabolic process / propionyl-CoA carboxylase / Defective HLCS causes multiple carboxylase deficiency / propionyl-CoA carboxylase activity / Biotin transport and metabolism / biotin binding / catalytic complex ...branched-chain amino acid metabolic process / succinyl-CoA biosynthetic process / Propionyl-CoA catabolism / short-chain fatty acid catabolic process / propionyl-CoA carboxylase / Defective HLCS causes multiple carboxylase deficiency / propionyl-CoA carboxylase activity / Biotin transport and metabolism / biotin binding / catalytic complex / fatty acid metabolic process / Mitochondrial protein degradation / mitochondrial matrix / enzyme binding / mitochondrion / metal ion binding / ATP binding / cytosol
Similarity search - Function
Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. ...Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Chem-BTI / Propionyl-CoA carboxylase alpha chain, mitochondrial / Propionyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsTian, X.Y. / Su, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071192 China
CitationJournal: To Be Published
Title: structure of human propionyl-coenzyme A carboxylase in BC binding state
Authors: Tian, X.Y. / Su, J.Y.
History
DepositionSep 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Propionyl-CoA carboxylase alpha chain, mitochondrial
B: Propionyl-CoA carboxylase alpha chain, mitochondrial
D: Propionyl-CoA carboxylase alpha chain, mitochondrial
F: Propionyl-CoA carboxylase alpha chain, mitochondrial
G: Propionyl-CoA carboxylase beta chain, mitochondrial
H: Propionyl-CoA carboxylase alpha chain, mitochondrial
I: Propionyl-CoA carboxylase beta chain, mitochondrial
J: Propionyl-CoA carboxylase alpha chain, mitochondrial
K: Propionyl-CoA carboxylase beta chain, mitochondrial
L: Propionyl-CoA carboxylase beta chain, mitochondrial
N: Propionyl-CoA carboxylase beta chain, mitochondrial
O: Propionyl-CoA carboxylase beta chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)774,65618
Polymers773,28612
Non-polymers1,3706
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Propionyl-CoA carboxylase alpha chain, mitochondrial / PCCase subunit alpha / Propanoyl-CoA:carbon dioxide ligase subunit alpha


Mass: 73723.312 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCCA / Production host: Homo sapiens (human) / References: UniProt: P05165, propionyl-CoA carboxylase
#2: Protein
Propionyl-CoA carboxylase beta chain, mitochondrial / PCCase subunit beta / Propanoyl-CoA:carbon dioxide ligase subunit beta


Mass: 55157.742 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCCB / Production host: Homo sapiens (human) / References: UniProt: P05166, propionyl-CoA carboxylase
#3: Chemical
ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human Propionyl-CoA carboxylase / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.828 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53676 / Symmetry type: POINT
RefinementHighest resolution: 3.53 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00255494
ELECTRON MICROSCOPYf_angle_d0.56975054
ELECTRON MICROSCOPYf_dihedral_angle_d8.0477842
ELECTRON MICROSCOPYf_chiral_restr0.0438526
ELECTRON MICROSCOPYf_plane_restr0.0049786

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